|
| Status |
Public on Mar 01, 2016 |
| Title |
control rep1 |
| Sample type |
SRA |
| |
|
| Source name |
control_Mandible
|
| Organism |
Mus musculus |
| Characteristics |
strain background: 129SvEv
developmental stage: embryonic day 10.5
genotype/variation: Yapf/f, Tazf/f
tissue: mandible
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
We dissected E10.5 mandibular tissues from Wnt1Cre Taz and Yap dKO mutant and control embryos in DEPC-treated PBS, then total RNA were extracted and treated for 30 min at 37˚C with RNAse free DNase I (Ambion). Poly(A) RNA was purified with the Micro Poly(A) purist Kit according to the manufacturer’s instructions (Ambion).
Purified RNA samples were processed for cDNA synthesis and library preparation following Ion Total RNA-Seq v2 (cat. #4475936) protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Torrent_Suite 4.0.2 for basecalling with parameters: `BaseCaller --keypass-filter on --phasing-residual-filter=2.0 --trim-qual-cutoff 15 --trim-qual-window-size 30 --trim-adapter-cutoff 16 --num-unfiltered 1000 --calibration-training=100000 --flow-signals-type scaled-residual --max-phasing-levels 2`
Sequenced reads were aligned against mouse genome mm9 using Tmap version 3.0.1 with default RNA-Seq setting `map4`
Gene expression levels were measured by counting numbers of reads in all the exons using HTSeq version 0.5.4p3 with parameters: `htseq-count -m union -s yes -t exon -i gene_symbol`
Differential gene expression was measured using DESeq version 1.16.0
Genome_build: mm9
Supplementary_files_format_and_content: comma-separated values files for raw read counts
Supplementary_files_format_and_content: comma-separated values files for differential gene expressionprofiling
|
| |
|
| Submission date |
May 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Min Zhang |
| E-mail(s) |
minzhang5099@gmail.com
|
| Organization name |
Baylor College of Medicine
|
| Department |
Department of Molecular Physiology
|
| Lab |
James F Martin
|
| Street address |
One Baylor Plaza Room 504E
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE69311 |
Yap and Taz in Neural Crest play a Crucial Role in Smooth Muscle Development |
|
| Relations |
| BioSample |
SAMN03738165 |
| SRA |
SRX1041265 |
